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Script that converts TRK to TCK using https://github.com/MarcCote/nibabel/tree/streamlines_tck
import os
import argparse
import nibabel as nib
def build_argparser():
DESCRIPTION = "Convert tractograms (TRK -> TCK)."
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument('tractograms', metavar='bundle', nargs="+", help='list of tractograms.')
p.add_argument('-f', '--force', action="store_true", help='overwrite existing output files.')
return p
def main():
parser = build_argparser()
args = parser.parse_args()
for tractogram in args.tractograms:
if nib.streamlines.detect_format(tractogram) is not nib.streamlines.TrkFile:
print("Skipping non TRK file: '{}'".format(tractogram))
continue
output_filename = tractogram[:-4] + '.tck'
if os.path.isfile(output_filename) and not args.force:
print("Skipping existing file: '{}'. Use -f to overwrite.".format(output_filename))
continue
trk = nib.streamlines.load(tractogram)
nib.streamlines.save(trk.tractogram, output_filename)
if __name__ == '__main__':
main()
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